On-the-fly, in-memory java code compilation for Java 5 and Java 6

JCI looks fine. This code snippet should be your base:

JavaCompiler compiler = new JavaCompilerFactory().createCompiler("eclipse");

MemoryResourceReader mrr = new MemoryResourceReader();
mrr.add("resource name string", yourJavaSourceString.getBytes());

MemoryResourceStore mrs = new MemoryResourceStore();

CompilationResult result = compiler.compile(sources, mrr, mrs);

// don't need the result, unless you care for errors/warnings
// the class should have been compiled to your destination dir

Any reason this should not work?

Also, setting javac settings, like classpath in your case, can be done via setCustomArguments(String[] pCustomArguments) in JavacJavaCompilerSettings class.

You might want to check out Janino as well.

From their website:

Janino is a compiler that reads a JavaTM expression, block, class body, source file or a set of source files, and generates JavaTM bytecode that is loaded and executed directly. Janino is not intended to be a development tool, but an embedded compiler for run-time compilation purposes, e.g. expression evaluators or "server pages" engines like JSP.

http://www.janino.net/

Im currently using it in a pretty large mission critical project and it works just fine